Samantha (she/her)
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Recent activity by Samantha (she/her) Sort by recent activity-
HI Jason Ni, Thank you for writing in about this issue. Can you share the workspace where you are seeing this issue with GATK/Terra Support by clicking the Share button in your workspace? The Share...
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Hi Kevin Meli, Thanks for reaching out. It looks like you've cloned a much older version of the GATK Somatic CNV workflow. The tools in the workflow have since been replaced, which is probably why ...
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Thanks, Philipp Hähnel. Wesley Kwong - are you able to resolve your issue with Philipp's advice? Best, Samantha
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I see. Can you temporarily share the gs://bruce-processed-data bucket with me (svelasqu@broadinstitute.org)? Even though the index file path isn't explicitly being passed to the GetPileupSummaries ...
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Hi Wesley Kwong, It looks like the error message in that submission is the one Genevieve pointed out in her latest message: A USER ERROR has occurred: Illegal argument value: Positional arguments w...
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Hi Wesley Kwong, Can you share the Submission ID so we can take a closer look at the issue? Best, Samantha
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Hi Oliver Ruebenacker, I've confirmed with the pipeline authors that the dbsnp file is indeed incorrect. I'll work on getting this updated in the featured workspace. Thank you for pointing this out...
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Hi Oliver Ruebenacker, Sorry for the delay. We are still looking into this and will let you know once we have an update. Best, Samantha
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Hi Oliver, Sorry for the delayed response. It does seem like there is an error in the Featured Workspace where the ref_name input for the 2-1-Processing-For-Variant-Discovery-B37 workflow is incorr...
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Hi Oliver Ruebenacker, Are you running the workflow on Terra? If so, can you share the workspace where you are seeing this issue with Terra Support by clicking the Share button in your workspace? T...